chr15-73924418-T-C

Position:

• chr15-73924418-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_040069.1(LOXL1-AS1):​n.184+3647A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,090 control chromosomes in the GnomAD database, including 2,344 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.16 (2344 hom., cov: 32)
• Consequence: LOXL1-AS1 NR_040069.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.79

Genes affected

LOXL1-AS1 (HGNC:44169): (LOXL1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOXL1-AS1	NR_040069.1	n.184+3647A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LOXL1-AS1	ENST00000685373.1	n.198+3359A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24377 AN: 151972 Hom.: 2348 Cov.: 32

Gnomad AFR AF: 0.0691

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.0232

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.165

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.160 AC: 24374 AN: 152090 Hom.: 2344 Cov.: 32 AF XY: 0.163 AC XY: 12135 AN XY: 74348

Gnomad4 AFR AF: 0.0691

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.0235

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.163

Alfa AF: 0.180 Hom.: 739

Bravo AF: 0.152

Asia WGS AF: 0.115 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	18
DANN	Benign	0.81

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs8026259; hg19: chr15-74216759;